NMR picoSpin User Guide - OSAKA...

NMR

picoSpin User Guide

269-298001 Revision A October 2013

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http://www.chem.wisc.edu/areas/reich/Handouts/nmr-h/hdata.htm

http://www.thermoscientific.com/picospin

C

Contents

Chapter 1 NMR SPECTROSCOPY . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1NMR Databases and Resources . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2

Chapter 2 System Operation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .3Web Browser Interface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3

Run . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3Files. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4Temperature . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5System. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6

Samples and Sample Preparation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6Viscosity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7Concentration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7Solvents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8

Sample Handling. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

Chapter 3 Experiment Scripts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .11onePulse . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11

Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12autoShim. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14

Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15Search . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16

Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17

Thermo Scientific picoSpin User Guide i

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ii picoSpin User Guide Thermo Scientific

1

NMR SPECTROSCOPY

Readers of the picoSpin User Guide should be familiar with the basics of pulsed NMR spectroscopy of liquids. An introduction to this subject can be found in any college-level organic chemistry textbook. There are also several excellent on-line resources available.

ReferencesThe Basics of NMR, by Joseph P. Hornak

Almost every section of this excellent text will be helpful to users of the picoSpin NMR spectrometers. The only sections that are not directly relevant are these: carbon-13, superconducting magnets, solid state, microscopy, and field cycling.

The NMR section of The Virtual Textbook of Organic Chemistry, by William Reusch

The basics in just a few pages.

NMR Web course, provided by Queen’s University, Ontario, CA, Department of Chemistry, and maintained by Francoise Sauriol, Ph.D.

Basic NMR concepts are covered as well as extensive coverage of pulse sequences. This site offers Shockwave animations.

NMR Tutor, by Charles B. Abrams

Interactive Flash animation of the basic concepts of NMR and pulse sequences.

NMR Lecture Course, by Hans Reich, Department of Chemistry, University of Wisconsin, Madison.

Advanced concepts in NMR.

Thermo Scientific picoSpin User Guide 1

http://www.cis.rit.edu/htbooks/nmr/

http://www2.chemistry.msu.edu/faculty/reusch/VirtTxtJml/Spectrpy/nmr/nmr1.htm#nmr1

http://www.chem.queensu.ca/facilities/nmr/nmr/webcourse/

http://faculty.ccc.edu/cabrams/projects/nmrtutor/NMR01.dcr

http://www.chem.wisc.edu/areas/reich/chem605/index.htm

1 NMR SPECTROSCOPYNMR Databases and Resources

NMR Databases and ResourcesSDBSWeb, provided by the National Institute of Advanced Industrial Science and Technology

This site provides a searchable database that includes 1H and 13C NMR spectra as well optical spectra.

WebSpectra, by Prof. Craig A. Merlic, UCLA Department of Chemistry and Biochemistry

Problems in NMR and IR Spectroscopy.

NMRShiftDB2, provided by the NMRShiftDB Project

These are searchable chemical shift databases for 1H, 13C, and other nuclei.

NMR Simulator, provided by NMRDB.org

A very nice interactive NMR simulator and database where one can draw structures and simulate their NMR spectra.

NMR Chemical Shift Tables, by Prof. Hans Reich, Department of Chemistry, University of Wisconsin, Madison.

A rich collection of chemical shift tables for 1H, 13C and other nuclei, as well as an extensive listing of J(HH) and J(CH) coupling constants.

2 picoSpin User Guide Thermo Scientific

http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/cre_index.cgi?lang=eng

http://www.chem.ucla.edu/~webspectra/

http://nmrshiftdb.nmr.uni-koeln.de/

http://www.nmrdb.org/

http://www.chem.wisc.edu/areas/reich/Handouts/nmr-h/hdata.htm

2

System Operation

Web Browser InterfaceThe web browser user interface of the picoSpin is accessed by pointing a web browser at the unit’s IP address, which is shown on the front-panel LCD display at power-up. An Ethernet connection can be made to the unit directly or through a local area network. See the Installation and Setup instructions to set up a connection.

We recommend Mozilla’s free Firefox™ web browser for best compatibility with our software, but most modern browsers will work nearly as well, including Google Chrome™ and Safari™. Internet Explorer™ is not supported.

When a web browser is pointed to http://xxx.xxx.xxx.xxx (where xxx.xxx.xxx.xxx is the unit’s IP address) the unit responds by displaying a splash screen with a large Thermo Scientific logo. You will be transferred to the Run page in a few seconds or you can go there immediately by clicking on the logo. If your connection is interrupted while you are operating the unit and the web interface becomes unresponsive, it may be helpful to return to the splash screen to restart the session.

The four main pages of the interface are Run, Files, Temperature and System. Orange links at the upper right of each page are used to navigate between them. A common message pane at the bottom of each page provides information about the currently running experiment and other operations. The content of the message pane is preserved when switching from one page to another.

Run

The Run page is used to choose and run experiment scripts, and to monitor their progress. The name of the currently loaded script is displayed in the upper left corner of the page. Next to the script name is an information button ( ) which will display information about the script.

The script and shims buttons are located at the top of the page. Clicking loads an experiment script with its most recently used settings. (To load a script with its default settings or with settings from a saved run, use the Files page.)


2 System OperationWeb Browser Interface

Click to display the settings of the magnet shim currents, which are real numbers between -1.0 and +1.0. By filling in the Shims Name field and clicking , you can save a shim settings file, which can be examined and selected on the Files page. Besides the three linear and five quadratic shims there are also fields for a uniform field shim and for a temperature. The temperature field on the Shim page has no effect on operation but it can be used to keep a record of the magnet temperature for which a particular set of shims is appropriate.

The Run page contains a list of script parameters, two data plots and (optionally) a Run Name field. The Show less/show more button can be used to display only the most important parameters or all parameters. The default condition of this button is determined by a preference setting on the System page. There are also preference settings to control whether the plots appear to the right of the parameters or beneath them, and whether the Run Name field appears at all. always appears near the top of the parameters list. This button changes to while a script is running, providing a way to interrupt an experiment.

The script parameter fields are defined by the loaded script. Each field has a name which appears to its left and some have a unit which appears to the right. Hovering the mouse pointer over the field name will bring up a brief description of the field. Most fields are checked for validity; if an invalid entry is made a flag will appear on the field. This flag must be cleared by correcting the entry before the script can be run.

If you type a name into the Run Name field and then click , a saved run will appear on the Files page after the script successfully completes. The saved run stores any data generated by the script and all of the settings.

The upper plot window is normally used for time-domain free induction decay (FID) data and the lower window is used to show the spectrum. However, scripts may use the plot windows in other ways.

Files

The Files page provides a way to examine and manipulate three kinds of information: saved runs with their data and settings, shim settings files, and scripts with default settings.

Menu Item Description

Run Data Last Run – stores the settings of the most recent data acquisition

Shims Current – stores the shims currently set on the Run page

Default – sets all shims to 0

Scripts autoShim – used for finding optimal magnet shim settings

onePulse –the experiment which will most often be used for collecting and analyzing data

Search – used for finding the Larmor frequency when the approximate frequency is not known


2 System OperationWeb Browser Interface

The saved runs appear beside the label Run Data. When Last Run is clicked the name of the script and the settings that were last used on the Run page are displayed. Below the settings appear any data files generated by the last run. The link Use these settings at Run will transfer operation to the Run page with the last-used script and all of its settings loaded. Clicking on a data file will bring up a download dialog. Buttons are provided to download all of the generated data ( ) and to delete the run ( ). The other saved runs behave similarly to Last Run. When any run is selected the time and date when it was saved appears to the right of the settings display.

Next to the Shims label the user can select the Current shims, the Default shims, or shims saved by experiment scripts. When a saved shim file is selected, buttons appear allowing the user to delete the file( ) or download it ( ). Downloaded shim files can be used to archive shim information. Saved shims can be moved to the Run page by clicking Use these settings at Run.

All experiment scripts currently available on the system appear next to the label Scripts. Clicking on a script name will display all of the settings fields with their names, default values, units and descriptions. Additional information about the script appears below the list of settings. To use the selected script at the run page with its default settings, click on Use default settings at Run. In most cases it is more convenient to select scripts by choosing a saved run or the last run.

Temperature

The Temperature page provides a convenient interface for the magnet temperature controller. The upper plot displays the magnet temperature in degrees Celsius, the middle plot shows the temperature of the magnet enclosure, and the lower plot shows the magnet heater setting. All plots show data over the previous six hours unless the unit has been on for less time or a system reset has ben performed. Click to reveal fields for setting the magnet temperature controller parameters. The settings normally used are: (picoSpin 45) Set Point = 42.0, P = 10.2, I = 0.02, heater = on, closed loop = on; (picoSpin 80) Set Point = 36.0, P = 10.5, I = 0.01. If closed loop = off the controller is disabled and the heater setting is determined by the output field. Controller settings are not changed until is clicked.

The magnet heater setting varies from 0 to 65535. If the heater setting shown in the bottom plot is at zero, the set-point temperature should be increased or the ambient temperature decreased. If the heater setting reaches its maximum value, the set-point temperature should be decreased or the ambient temperature increased.

When the unit has been turned off and then turned on, it may take from 30 minutes to 4 hours for the magnet temperature to heat up and stabilize. During this time it is normal for the heater setting to first be at zero and then to swing abruptly to its maximum value. Settings should not be adjusted until the system has stabilized.


2 System OperationSamples and Sample Preparation

System

Click the Preferences link to display three check boxes that can be used to control the display of information on the Run page. The Run Name box determines if a Run Name field appears above the script parameters. Checking this box enables saving of named runs. The Expert Mode box controls the starting condition of the show more/show less button. The Display Plots at Right button controls the position of the data plots relative to the parameters list.

The Settings link provides access to fields for setting the default IP address which is used when DHCP is not available. This IP address will not become effective until power is switched off and back on or the web server CPU is restarted. It will appear on the front panel LCD display after power-on or restart only if no DHCP server is available. The date, time and time zone may also be set under the Settings link. The clock time is used to label saved runs and data files.

The currently installed software and firmware versions may be inspected by clicking on the Version link.

Click the Restart link to restart the web server CPU inside the spectrometer. This should be done with caution when operating remotely since it will interrupt the web browser connection.

The System Update link is used to update the system software, including the web browser interface. Click this link only when you have received an update file and installation instructions from us.

Samples and Sample PreparationWARNING Avoid personal injury.

• Needles and syringes should be considered regulated waste regardless of use

• Follow your local EH&S guidelines for disposal

• Never throw these items into the regular trash or dumpsters

CAUTION Avoid personal injury.

•Wear eye protection at all times when handling liquid chemicals

•Do not breathe hazardous vapors

•Avoid skin contact with hazardous liquids and vapors

•Eliminate ignition sources and prevent significant waste volume buildup



Viscosity

The 300 micron inside diameter of the cartridge tubing limits the viscosity of the sample one can inject without exceeding the approximately 100 PSI upper pressure limit. If you have difficulty drawing the sample into the injection syringe you will likely also have difficulty injecting it into the cartridge inlet. Adding a small amount of an inviscid solvent may dramatically reduce the viscosity of a sample. Liquids with kinematic viscosity of 40 cSt (centistokes) to 45 cSt at approximately 35 °C to 40 °C represent the upper limit on sample viscosity before dilution should be considered. For reference, cooking oils such as olive oil have viscosities of 35 cSt to 45 cSt in the temperature range from room temperature to approximately 45 °C. Online viscosity tables may be consulted for guidance on other common liquids.

Concentration

The signal strength in proton NMR spectroscopy is directly proportional to the concentration of hydrogen nuclei in the sample. To maximize the signal-to-noise ratio (SNR), samples should be prepared with the highest possible concentration of the analyte of interest. In some situations, following this guidance may lead to samples which are too viscous or which have broadened spectral features. In these cases, begin with the highest possible concentration and then add solvent as necessary.

The exact SNR depends on the quality of the magnet shim, the data acquisition parameters and on choices made when filtering or apodizing the data. (picoSpin documentation uses the spectroscopic definition of signal-to-noise ratio: maximum height of the peak divided by the root-mean-square noise of the baseline.) In exceptional cases, the SNR may also depend on intrinsic sources of peak broadening. However, it is usually possible to estimate the SNR by comparison with the signal from pure water. We have specified SNR for pure water for a single scan. (Consult the factory test report for the water SNR measured with your unit at the factory.) Since the SNR is directly proportional to concentration, you can scale from pure water to estimate the SNR for any spectral peak. The concentration of water molecules in pure water is 55 M (55 moles/liter). When scaling it is necessary to include a factor for the “weight” of the peak of interest relative to the water peak. The weight is the number of protons per molecule contributing to the peak multiplied by the peak’s normalized intensity within the multiplet. (The normalized intensity is 1 for a singlet, 1/2 for each peak of a doublet, 1/2 for the middle peak of a triplet and 1/4 for the outer peaks of a triplet.) For example, the water singlet has a weight of 2*1=2, a CH3 singlet has a weight of 3*1=3 and one peak in a CH3 doublet has a weight of 3*1/2=1.5.)

Suppose, for example, that the analyte molecule has a concentration of 0.55 M and we would like to estimate the SNR of one peak in a CH3 doublet. If the single-scan SNR for pure water is 1,000, the result will be 1,000*(0.55/55)*(1.5/2) = 7.5 (for the picoSpin 45). The single-scan SNR can be increased by averaging many scans. Because the SNR increases as the square root of the number of scans, it is not generally practical to increase it by more than a factor of 30 above the single-scan value; in most cases, the sample concentration should be increased if the estimated single-scan SNR of an important peak is less than 1.



Neat liquid samples are the most favorable case. They should generally be analyzed without dilution unless peak broadening or viscosity problems are a known concern.

In most cases, an SNR estimate, like the one described above, will show that multicomponent homogeneous mixtures should have a concentration of at least 1% by volume.

Solid samples must be fully dissolved in a suitable solvent. The effective lower limit on sample concentration is approximately 0.5 M for the picoSpin 45 and 0.2 M for the picoSpin 80, as shown by the estimation method above. Since only about 30 to 40 μL of sample is needed, one typically needs to mix only about 250 μL of solution. Many small organic molecules being analyzed have a molar mass between 100 and 300 g/mol. To make a 1 M solution, 25 to 75 mg of material needs to be dissolved in 250 μL of solution.

Solvents

Where solid samples are concerned, either deuterated or undeuterated solvents may be used to prepare sample solutions for analysis. Deuterated solvents are more expensive, more difficult to obtain, and their light and moisture sensitivity tend to limit their shelf life. Protonated solvents can be used if the proton solvent signals do not overlap or otherwise interfere with other signals of interest. If a protonated solvent cannot be used, then one should select a deuterated NMR solvent which affords the highest solution concentration for sample analysis. In selecting a deuterated solvent one should keep four considerations in mind:

Concentration — To achieve the highest quality spectrum one should choose the deuterated solvent for which the solute has the highest solubility. Note that chemical shifts can depend somewhat on sample concentration and the solvent environment.

Proton-deuterium (H-D) exchange — When using a deuterated solvent one must be aware of the presence of labile or acidic protons in the sample which can suffer from H-D exchange with the solvent. H-D exchange has the effect of removing signals from the NMR spectrum, and sometimes this is a desirable effect. For partial or incomplete H-D exchange a residual proton signal may still be present and can affect integration ratios. The most common functional groups that undergo H-D exchange are hydroxyl (-OH), amine (-NH, -NH2), thiol (-SH, -SH2), and carboxylic acid (-CO2H) groups.

Solvent polarity — The chemical shift and spin-spin splitting of proton NMR signals can depend on the dielectric constant of the solvent. There are many excellent texts which describe applications where one can benefit from a judicious choice of solvent.

NMR solvents which are most commonly used are: CDCl3, C6D6, D2O, acetone-d6, DMSO-d6, MeOD and methanol-d4. Since the magnet is typically temperature stabilized at 36 °C (picospin 80) or 42 °C (picoSpin 45), methylene chloride-d2(CD2Cl) cannot be used directly in the picoSpin due to its low boiling point (39.75 °C). It can still be used as a co-solvent. Many NMR solvents can be purchased with added internal reference substances, such as DSS (4,4-dimethyl-4-silapentane-1-sulfonic acid) for D2O or TMS (tetramethylsilane) for organic solvents, and which are defined to have a chemical shift of 0 ppm. NMR solvents with 1% TMS are desirable when an internal reference is needed.


2 System OperationSample Handling

Sample HandlingSamples may be manually injected into the picoSpin using a glass syringe, as shown in Figure 1, or using a polypropylene syringe, as shown in Figure 2. Gas-tight glass syringes are recommended for general laboratory use, but plastic syringes may be preferred for teaching purposes or when it is not practical to re-use a glass syringe.

Figure 1. Sample injection with a glass syringe

Figure 2. Sample injection with a plastic syringe

Complete sets of sample handling supplies are available from us. The Laboratory Kit contains a gas-tight glass syringe and related accessories, while the Teaching Kit contains plastic syringe accessories. Full documentation for these kits is available on our web site.

Sample handling accessories must be compatible with the cartridge fittings. The inlet is a 1/16-inch stainless steel bulkhead fitting with an external stainless steel frit filter.


2 System OperationSample Handling

Glass syringe accessories suitable for use with the picoSpin are shown in Figure 3. The 100 μL syringe has a PTFE gas-tight plunger and a removable 26-gauge blunt-tip needle. The needle is inserted into a syringe port. The drain tube uses a PEEK nut, a grooved PEEK ferrule, and a length of 30-gauge PTFE 0.030-inch OD tubing. The ferrule has been crimped onto the PTFE tubing by inserting it into a mating fitting and tightening the retaining nut 1-1/4 turns.

Figure 3. Glass gas-tight syringe and other accessories for sample injection

An example set of plastic syringe accessories is shown in Figure 4. The 1 mL polypropylene syringes are shown with optional 0.22 μm PTFE filters. Connection to the inlet fiting is made with a syringe port.

Figure 4. Plastic syringe and accessories

100 μL syringe22-gauge blunt tip needle

Inlet filter with plug

Syringe port

PEEK Plugs

Drain tube assembly

Syringe filter, PTFE,0.22 μm, 13 mm

22-gauge blunt tip needleInlet filter with plug

PEEK plugs

Drain tube assembly

1 mL polypropylene syringe

Syringe ports


3

Experiment Scripts

All experiments on the picoSpin spectrometers are implemented by means of factory defined scripts. The scripts are responsible for loading pulse sequences to the NMR Engine, retrieving data from the NMR Engine, and sending the data to the embedded web server for plotting to a browser window. Optionally the scripts may do a range of other tasks such as communicate with the shim controller, the temperature controller, or the LCD display.

There are three scripts distributed with the spectrometer software: onePulse, autoShim, and Search. Of the three only the onePulse script is generally used to acquire data. The Search and autoShim scripts are used to find the Larmor frequency of the sample and improve the peak shape, respectively.

onePulseThe onePulse script is the experiment which will most often be used for collecting and analyzing data. It implements a single-pulse acquisition sequence as shown in Figure 5.

Figure 5. onePulse pulse sequence

The sequence transmits a single pulse, waits for a receiver recovery delay time, then begins recording data. The sequence is executed in the NMR Engine hardware so its timing is highly deterministic. Once the sequence is complete, the onePulse script retrieves the data from the NMR Engine, processes it, and sends the data to the browser window and/or JCAMP-DX file if requested. If the user has requested multiple scans, the script then checks how much time


3 Experiment ScriptsonePulse

has elapsed since the start of the last pulse sequence and attempts to wait the necessary time as defined by the T1 recovery delay before attempting to start the next sequence. If the target time has already passed due to the time it took to do the processing, the script will report to the message window, “processing extended repetition delay by x seconds”. If the specified T1 recovery time is long enough for the script to start the next acquisition sequence in the requested time, a statement indicating “processing complete; waiting x s before sequence repeat” will be shown in the message window.

When multiple scans are acquired the user has the choice to save the data from each pulse separately or to have the data averaged together. To achieve the best possible resolution it is necessary to align the data before subsequent spectra are averaged. With the onePulse script, when spectra are averaged, the data are always aligned before averaging. The alignment algorithm requires that there be at least one high SNR peak present in the spectrum. If you are trying to observe a very low SNR peak by averaging many scans, make sure there is at least one high SNR peak present elsewhere in the spectrum.

Parameters

tx frequency — The RF transmitter frequency specified in MHz. This frequency corresponds to the 0, or center, frequency of the spectral plot.

scans — The number of times to run the single-pulse acquisition sequence. If a certain target SNR is desired, run the script with a small number of scans at first to estimate the SNR per scan. Then compute the number of scans needed assuming that the SNR will increase as the square root of the number of scans.

pulse width — The duration of the RF pulse in microseconds.

acq. pts —The number of points to acquire per acquisition. The acquisition time is this number divided by the specified bandwidth.

rx recovery delay — The time between the end of the pulse and the beginning of data acquisition. This delay time allows the system to recover from ring-down and RF switch transients.

T1 recovery delay — The requested T1 recovery time between experiments. Since this is implemented at the script level the actual time between pulse-acquisitions will be extended if processing or server overhead require more time.

bandwidth — The bandwidth of the receiver channel. This number determines the dwell time of the data acquisition. It is the rate in kHz at which the digitizer samples the signal.

post-filter atten. — The attenuation setting of the filter electronics.

phase correction — The amount of zeroth-order phase correction to apply.

exp. filter — If non-zero, applies an exponential apodization to the time series data (FID) specified in hertz. This parameter only effects displayed data and not saved data.


3 Experiment ScriptsonePulse

max plot points — The maximum number of points to plot to the browser. If fewer points are specified than the number of acquisition points, the script will attempt to decimate the FID and spectral data down to a number of points which does not exceed this number. If greater than the number of acquisition points are specified, the script will plot the number of acquisition points to the browser. The purpose of this parameter is to decrease the load on the operating system. This may improve the ability of the operating system to accommodate the user specified T1 recovery delay request. This parameter does not affect the number of points saved to data files.

max time to plot — The maximum time to plot for time series data (FID) in the browser. This parameter is useful when the user wants a long acquisition time but wants to have a zoomed in look at the beginning of the FID. This parameter does not affect the number of points saved to the data files.

min freq. to plot — The minimum frequency to plot for spectral data in the browser. This parameter is useful when the user only wants to look at part of the acquired spectrum. This parameter does not affect the number of points saved to data files.

max freq. to plot — The maximum frequency to plot for spectral data in the browser. This parameter is useful when the user only wants to look at part of the acquired spectrum. This parameter does not affect the number of points saved to data files.

zero filling — The number of Fourier transform points to use when aligning data by cross-correlation. Generally the aligning routine performs better the greater the number of points, but the longer the processing time required, which may affect the T1 relaxation delay request. Using a value which is the nearest power of 2 greater than four times the number of acquisition points works well for most cases. For example if 1000 points are acquired per scan then setting this to 4096 would produce a good alignment. If zero filling is less than Acq pts then twice the number of acquisition points are used for the alignment routine.

align-avg. data — Whether to align and average data that is acquired. The alignment routine performs a cross-correlation between the current scan and the aligned average of the previous scans before averaging the two together. When setting this parameter also be aware of setting zero filling appropriately.

live plot — Plots data to the browser for each scan acquired. Unchecking this parameter may improve the ability of the operating system to accommodate the user’s requested T1 recovery delay.

JCAMP avg. — If align-avg data is set, this parameter determines whether a JCAMP-DX file of the aligned and averaged data is saved for the run.

JCAMP ind. — Determines whether to write individual JCAMP-DX files for each scan for processing with the user’s analysis software.


3 Experiment ScriptsautoShim

autoShimThe picoSpin contains a set of eight shim coils for improving the field homogeneity plus a ninth coil to apply a uniform z field. These coils are contained in the user replaceable cartridge which is included in the unit. The cartridge implements the following magnetic field gradients:

first order• x• y • z

second order• zx • zy • xy• z2

• x2 - y2

zeroth order

• B0

The orientation of the coordinate system is such that y is coaxial with the capillary (perpendicular to the front face of the instrument), x is perpendicular to the side face, and z is perpendicular to the base.

Due to very slight differences between magnets, shim cartridges, and shim electronics, different hardware components need different shim parameters. Although these shims can be set with the shim drop-down of the browser interface, this script automates the task. To do this it implements the Nelder-Mead (simplex) optimization algorithm to find the set of shim values which maximize the quality of the peak.

We refer to the size of the steps that the algorithm starts off with as increments. To reduce the complexity of the user interface it is only necessary to specify the size of the increments to use for all the first order (linear) shims and the size of the increments to use for the second order (quadratic) shims. If either of these are zero, that set of shims will be excluded from the optimization.

While the script is running the message window indicates the shim values that are being tried by the optimization algorithm and the LCD displays the iteration number of the simplex routine on the first line and the best value for the quality of the peak on the second line. The script also keeps a log file of all the shim values tried, the associated quality value, and the frequency of that peak.


3 Experiment ScriptsautoShim

When the script stops, either because it has reached the maximum number of iterations specified, it has passed the convergence criterion, or the run has been aborted, the best values of the shims found will be saved and will appear in the shim drop-down of the browser interface. The next time any script is run these will be the shim values used unless manually changed.

The shims found by the script can be saved to a file with the shims drop down on the Run page, entering a Shims Name, and clicking . Check to make sure the Shims Name field is clear when starting a new autoShim run or your previously saved shim could be overwritten.

Parameters

tx frequency — The RF transmitter frequency specified in MHz. This frequency corresponds to the 0, or center, frequency of the spectral plot.

max iterations — The maximum number of times the Nelder-Mead algorithm should evaluate the simplex during the search. This is a number that is less than the number of times the data acquisition sequence is actually run because the routine may need to evaluate the quality of the signal at several shim settings for each iteration.

test run — Whether to do a test run of the current script parameters and shim settings. No actual changes are made to the shims. This is provided as a convenient way to check that the acquisition parameters and location of the signal are suitable before actually trying to perform automatic shimming.

linear increments — The initial step size to use for the first-order shims in the Nelder-Mead method.

quadratic increments — The initial step size to use for the second-order shims in the Nelder-Mead method.

target rms — The criterion for convergence of the automatic shimming algorithm. When the algorithm reaches this value the script stops and reports the best shims found in the order shown at the beginning of the description of this script.


acq. pts — The number of points to acquire during an acquisition. The acquisition time is this number divided by the specified bandwidth.

zero filling — The number of points to use for zero filling of the time series data (FID). Increasing this number beyond the number of acquisition points improves in the estimates of the tallest peak’s Larmor frequency and signal strength used by the script.




3 Experiment ScriptsSearch

rx recovery delay — The time between the end of the pulse and the beginning of data acquisition. This delay time allows the system to recover from ringdown.

T1 recovery time — The requested T1 recovery time between acquisitions. Since this is implemented at the script level the actual time between pulse-acquisitions is nondeterministic.

phase correction — The amount of zeroth-order phase correction to apply.

exp. filter — If non-zero, applies an exponential apodization to the time series data (FID) specified in Hertz. This parameter only affects the displayed spectrum and not the saved data.

max plot points — The maximum number of points to plot to the browser. If fewer points are specified than the number of acquisition points, the script will attempt to decimate the time and spectral data down to a number of points which does not exceed this number. If greater than the number of acquisition points are specified, the script will plot the number of acquisition points to the browser. The purpose of this parameter is to decrease the load on the operating system. This may improve the ability of the operating system to accommodate the user specified T1 recovery delay request. This parameter does not affect the number of points saved to data files.

max time to plot — The maximum time to plot for the time series data (FID) in the browser. This parameter is useful when the user wants a long acquisition time but wants to look at the beginning of the FID in detail. This parameter does not affect the number of points saved to data files.


max freq to plot — The maximum frequency to plot for spectral data in the browser. This parameter is useful when the user only wants to look at part of the acquired spectrum. This parameter does not affect the number of points saved to data files.

magnitude — If set, uses the RMS spectral magnitude in the optimization routine instead of the intensity of the real part of the signal. This avoids having to worry about changes of phase when using large shim search increments.

SearchThe search script is used to find the Larmor frequency of the sample. It is often used when a new cartridge has been installed in the spectrometer or the temperature set point of the magnet has been changed. The pulse sequence this script loads to the NMR Engine is the same as the onePulse script. The difference is that this script steps the transmitter frequency before running the sequence and checks the spectrum for a peak that passes a user specified signal-to-noise ratio (SNR) criterion. The SNR is calculated by taking the magnitude of the tallest peak and dividing by the standard deviation of the points in a user specified window of



the real part of the spectrum. No checking is done to see whether the peak itself is in that window, so the frequency step size should be chosen to be less than the acquisition bandwidth and probably greater than the width of the noise window. While the script is running the LCD indicates the current frequency that is being probed.

In situations where the signal is very strong it may be possible that the SNR criterion is exceeded for an aliased signal. This might be the case the system is already shimmed well. Therefore when a search stops because a signal was found it may be worthwhile to use the onePulse script with transmitter frequencies which push the signal to the left or right side of the acquisition bandwidth to see that whether the signal is reduced in amplitude or vanishes altogether. If the signal gets larger instead, the original window displayed an aliased signal.

Parameters

start frequency — The frequency in MHz at which to begin the search.

stop frequency — The frequency in MHz at which the search is to end.

frequency step — The size of the frequency steps in kHz to take during the search. Negative or positive values are allowed, appropriate to the starting and stopping frequencies, to scan either up or down in frequency.

SNR — The signal-to-noise ratio at which the search will consider that it has found a peak. When this threshold is exceeded the search stops and the message window reports the magnitude, SNR, and frequency of the tallest peak found.

noise window start — The frequency of the lower limit of the noise window for estimation of SNR. Due to the discrete nature of the spectrum, the actual frequency boundary may differ. The message window will indicate the actual frequency used.

noise window end — The frequency of the upper limit of the noise window for estimation of SNR. Due to the discrete nature of the spectrum, the actual frequency boundary may differ. The message window will indicate the actual frequency used.


acq. pts — The number of points to acquire during an acquisition. The acquisition time is this number divided by the specified bandwidth.

rx recovery delay — The time between the end of the pulse and the beginning of acquisition to wait for the receiver electronics to recover from ring down.

T1 recovery time — The requested T1 recovery time between acquisitions. Since this is implemented at the script level the parameter is non-deterministic.





phase correction — The amount of phase correction to apply to the spectral data (FID) in degrees. This parameter only affects the displayed phase and not the phase of saved data.

exp. filter — If non-zero, applies an exponential apodization to the time series data (FID) specified in Hertz. This parameter only affects the displayed spectrum and not saved data.

max plot points — The maximum number of points to plot to the browser. If fewer points are specified than the number of acquisition points, the script will attempt to decimate the time and spectral data down to a number of points which does not exceed this number. If greater than the number of acquisition points are specified, the script will plot the number of acquisition points to the browser. The purpose of this parameter is to decrease the load on the operating system. This may improve the ability of the operating system to accommodate the user specified T1 recovery time. This parameter does not affect the number of points saved to data files.

max time to plot — The maximum time to plot for the time series (FID) data in the browser. This parameter is useful when the user wants a long acquisition time but wants to look at the beginning of the FID in detail. This parameter does not affect the number of points saved to data files.


max freq. to plot — The maximum frequency to plot for spectral data in the browser. This parameter is useful when the user only wants to look at part of the acquired spectrum. This parameter does not affect the number of points saved to data files.

live plot — Plots data to the browser for each scan acquired. Unchecking this parameter may improve the ability of the operating system to accommodate the user’s requested T1recovery delay.

magnitude — Whether to plot the spectral magnitude along with the real part of the spectrum.


NMR picoSpin User Guide - OSAKA...

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